The Unz Review: An Alternative Media Selection
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 TeasersGene Expression Blog

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You have probably seen these animations at some point, but if not, I encourage you to check them out. They certainly make abstractions such as DNA → RNA → Protein “come to life.” Below you have transcription, and then translation.

Though the DNA replication visualization is probably the most impressive to me:

The Walter & Eliza Hall Institution of Medical Research has about a dozen animations of this sort. Molecular Movies has a great many, though some of them are more like animated GIFs. Much respect for this group for putting these videos out there, as I see them being used without attribution all over YouTube (with different voice overs, etc.).

In population and phylogenetics visuzliation of complex data has become extremely important in imparting understanding even to specialist audiences. One of the problems for me in relation to molecular genetics papers has always been that verbal description and static schematic figures often do not capture in vivid enough detail the models being outlined. It seems that in the future better visualization tools might allow for more ubiquitous utilizations of three dimensional animation to illustrate structural mechanistic models.

• Category: Science • Tags: Genetics, Molecular Genetics, Visualization 
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I’ve been playing around with ADMIXTURE and EIGENSOFT with the the HapMap data set along with a few friends & family merged into it. It is interesting to see how the intuitive inferences you make from ADMIXTURE bar plots differ somewhat from PCA scatter plots. In any case, I’ve been posting some of the preliminary results on Facebook (in part because one of my friends is on Facebook and is curious about his own genetic background), and a friend who is a grad student pointed me to Structurama, which infers the best number of categories* (one can do cross-vaidation in ADMIXTURE). I’ve avoided STRUCTURE because it’s computationally more intensive. Any other recommendations? Specifically, something not mentioned by Dienekes or David.

Below the fold is a taste of the games my computer has been up to overnight. K = 5 ancestral populations in ADMIXTURE. HapMap Utah whites, Tuscans, Mexicans, Beijing Chinese, in that order. The last 6 bars are: my father, my mother, and then four individuals of European ancestry, Euro 1, Euro 2, Euro 3, and Euro 4. After merging files and pruning founders and thinning the markers to reduce linkage disequilibrium I was left with 120,000 SNPs. Just a note, I’ve played around with different numbers of SNPs at various K’s, and some very small differences are surprising consistent. My mother is always just a bit more “Asian” than my father.

* Some of the download links on the Structurama site do not seem to work right now, but you can download the source code. Didn’t try the Mac links.

• Category: Science • Tags: Genetics, Genomics, Visualization 
Razib Khan
About Razib Khan

"I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. If you want to know more, see the links at"